Methyl dynamics in crystalline amino acids: MD and NMR

J Comput Chem. 2003 Jul 15;24(9):1052-8. doi: 10.1002/jcc.10263.

Abstract

Correlation times for rotation of deuterated methyls in crystalline leucine, valine, and cyclo-L-alanyl-L-alanine are calculated with molecular dynamics and compared with NMR data. The simulations distinguish between methyls having different steric environments in the crystal, yielding correlation times differing by a factor of up to 30 for methyls within a given crystal. MD and NMR correlation times agree to within a factor of 2. However, averaging over nonequivalent methyls can yield correlation functions that, although actually multiexponential, are well fit by single exponentials. This may have significance for interpreting NMR data; previous NMR data did not distinguish between the methyls in these crystals. Adiabatic rotational barriers calculated with the X-ray structure differ from effective barriers during simulation by up to +/-1 kcal/mol; the difference indicates that dynamical effects have a significant role in determining rotational correlation times.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Amino Acids / chemistry*
  • Computer Simulation*
  • Crystallography, X-Ray
  • Leucine / chemistry
  • Methane / chemistry
  • Nuclear Magnetic Resonance, Biomolecular
  • Peptides, Cyclic / chemistry
  • Protein Conformation
  • Thermodynamics
  • Valine / chemistry

Substances

  • Amino Acids
  • Peptides, Cyclic
  • cyclo(alanylalanyl)
  • Leucine
  • Valine
  • Methane